A citation-based method for searching scientific literature

Kristopher W Brannan, Isaac A Chaim, Ryan J Marina, Brian A Yee, Eric R Kofman, Daniel A Lorenz, Pratibha Jagannatha, Kevin D Dong, Assael A Madrigal, Jason G Underwood, Gene W Yeo. Nat Methods 2021
Times Cited: 15







List of co-cited articles
99 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


A large-scale binding and functional map of human RNA-binding proteins.
Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M Blue, Jia-Yu Chen, Neal A L Cody, Daniel Dominguez,[...]. Nature 2020
227
26

Single-cell Ribo-seq reveals cell cycle-dependent translational pausing.
Michael VanInsberghe, Jeroen van den Berg, Amanda Andersson-Rolf, Hans Clevers, Alexander van Oudenaarden. Nature 2021
16
26


RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins.
Nicole Lambert, Alex Robertson, Mohini Jangi, Sean McGeary, Phillip A Sharp, Christopher B Burge. Mol Cell 2014
225
20

HITS-CLIP: panoramic views of protein-RNA regulation in living cells.
Robert B Darnell. Wiley Interdiscip Rev RNA 2010
277
20

irCLIP platform for efficient characterization of protein-RNA interactions.
Brian J Zarnegar, Ryan A Flynn, Ying Shen, Brian T Do, Howard Y Chang, Paul A Khavari. Nat Methods 2016
136
20

Atlas of Subcellular RNA Localization Revealed by APEX-Seq.
Furqan M Fazal, Shuo Han, Kevin R Parker, Pornchai Kaewsapsak, Jin Xu, Alistair N Boettiger, Howard Y Chang, Alice Y Ting. Cell 2019
204
20

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Eric L Van Nostrand, Gabriel A Pratt, Alexander A Shishkin, Chelsea Gelboin-Burkhart, Mark Y Fang, Balaji Sundararaman, Steven M Blue, Thai B Nguyen, Christine Surka, Keri Elkins,[...]. Nat Methods 2016
585
20

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins.
Aoife C McMahon, Reazur Rahman, Hua Jin, James L Shen, Allegra Fieldsend, Weifei Luo, Michael Rosbash. Cell 2016
101
20

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
20

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
20

TRIBE editing reveals specific mRNA targets of eIF4E-BP in Drosophila and in mammals.
Hua Jin, Weijin Xu, Reazur Rahman, Daxiang Na, Allegra Fieldsend, Wei Song, Shaobo Liu, Chong Li, Michael Rosbash. Sci Adv 2020
11
27

Translation dynamics of single mRNAs in live cells and neurons.
Bin Wu, Carolina Eliscovich, Young J Yoon, Robert H Singer. Science 2016
259
20

CUT&Tag for efficient epigenomic profiling of small samples and single cells.
Hatice S Kaya-Okur, Steven J Wu, Christine A Codomo, Erica S Pledger, Terri D Bryson, Jorja G Henikoff, Kami Ahmad, Steven Henikoff. Nat Commun 2019
432
20


Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
Markus Hafner, Markus Landthaler, Lukas Burger, Mohsen Khorshid, Jean Hausser, Philipp Berninger, Andrea Rothballer, Manuel Ascano, Anna-Carina Jungkamp, Mathias Munschauer,[...]. Cell 2010
13

A census of human RNA-binding proteins.
Stefanie Gerstberger, Markus Hafner, Thomas Tuschl. Nat Rev Genet 2014
988
13

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.
Bastian Linder, Anya V Grozhik, Anthony O Olarerin-George, Cem Meydan, Christopher E Mason, Samie R Jaffrey. Nat Methods 2015
715
13

CLIP identifies Nova-regulated RNA networks in the brain.
Jernej Ule, Kirk B Jensen, Matteo Ruggiu, Aldo Mele, Aljaz Ule, Robert B Darnell. Science 2003
770
13

HITS-CLIP yields genome-wide insights into brain alternative RNA processing.
Donny D Licatalosi, Aldo Mele, John J Fak, Jernej Ule, Melis Kayikci, Sung Wook Chi, Tyson A Clark, Anthony C Schweitzer, John E Blume, Xuning Wang,[...]. Nature 2008
941
13

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Julian König, Kathi Zarnack, Gregor Rot, Tomaz Curk, Melis Kayikci, Blaz Zupan, Daniel J Turner, Nicholas M Luscombe, Jernej Ule. Nat Struct Mol Biol 2010
727
13

Methods to study RNA-protein interactions.
Muthukumar Ramanathan, Douglas F Porter, Paul A Khavari. Nat Methods 2019
122
13



A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine.
L M Powell, S C Wallis, R J Pease, Y H Edwards, T J Knott, J Scott. Cell 1987
824
13

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs.
Brad R Rosenberg, Claire E Hamilton, Michael M Mwangi, Scott Dewell, F Nina Papavasiliou. Nat Struct Mol Biol 2011
163
13

Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon.
S H Chen, G Habib, C Y Yang, Z W Gu, B R Lee, S A Weng, S R Silberman, S J Cai, J P Deslypere, M Rosseneu. Science 1987
611
13

Differential Requirements for eIF4E Dose in Normal Development and Cancer.
Morgan L Truitt, Crystal S Conn, Zhen Shi, Xiaming Pang, Taku Tokuyasu, Alison M Coady, Youngho Seo, Maria Barna, Davide Ruggero. Cell 2015
206
13

RNA-Binding Proteins in Cancer: Old Players and New Actors.
Bruno Pereira, Marc Billaud, Raquel Almeida. Trends Cancer 2017
328
13

The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells.
Shuibin Lin, Junho Choe, Peng Du, Robinson Triboulet, Richard I Gregory. Mol Cell 2016
791
13

N6-methyladenosine-dependent regulation of messenger RNA stability.
Xiao Wang, Zhike Lu, Adrian Gomez, Gary C Hon, Yanan Yue, Dali Han, Ye Fu, Marc Parisien, Qing Dai, Guifang Jia,[...]. Nature 2014
13

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
13


Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
13

Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).
Eric L Van Nostrand, Thai B Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M Blue, Gabriel A Pratt, Ashley L Louie, Gene W Yeo. Methods Mol Biol 2017
35
13

Targeting the RNA m6A Reader YTHDF2 Selectively Compromises Cancer Stem Cells in Acute Myeloid Leukemia.
Jasmin Paris, Marcos Morgan, Joana Campos, Gary J Spencer, Alena Shmakova, Ivayla Ivanova, Christopher Mapperley, Hannah Lawson, David A Wotherspoon, Catarina Sepulveda,[...]. Cell Stem Cell 2019
193
13

Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.
Emily C Wheeler, Anthony Q Vu, Jaclyn M Einstein, Matthew DiSalvo, Noorsher Ahmed, Eric L Van Nostrand, Alexander A Shishkin, Wenhao Jin, Nancy L Allbritton, Gene W Yeo. Nat Methods 2020
27
13

ER stress-mediated autophagy promotes Myc-dependent transformation and tumor growth.
Lori S Hart, John T Cunningham, Tatini Datta, Souvik Dey, Feven Tameire, Stacey L Lehman, Bo Qiu, Haiyan Zhang, George Cerniglia, Meixia Bi,[...]. J Clin Invest 2012
267
13

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
13

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13

Epithelial-to-mesenchymal transition activates PERK-eIF2α and sensitizes cells to endoplasmic reticulum stress.
Yu-Xiong Feng, Ethan S Sokol, Catherine A Del Vecchio, Sandhya Sanduja, Jasper H L Claessen, Theresa A Proia, Dexter X Jin, Ferenc Reinhardt, Hidde L Ploegh, Qiu Wang,[...]. Cancer Discov 2014
174
13

The RNA m6A Reader YTHDF2 Maintains Oncogene Expression and Is a Targetable Dependency in Glioblastoma Stem Cells.
Deobrat Dixit, Briana C Prager, Ryan C Gimple, Hui Xian Poh, Yang Wang, Qiulian Wu, Zhixin Qiu, Reilly L Kidwell, Leo J Y Kim, Qi Xie,[...]. Cancer Discov 2021
83
13

Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
Jaclyn M Einstein, Mark Perelis, Isaac A Chaim, Jitendra K Meena, Julia K Nussbacher, Alexandra T Tankka, Brian A Yee, Heyuan Li, Assael A Madrigal, Nicholas J Neill,[...]. Mol Cell 2021
27
13

Trans-acting translational regulatory RNA binding proteins.
Robert F Harvey, Tom S Smith, Thomas Mulroney, Rayner M L Queiroz, Mariavittoria Pizzinga, Veronica Dezi, Eneko Villenueva, Manasa Ramakrishna, Kathryn S Lilley, Anne E Willis. Wiley Interdiscip Rev RNA 2018
47
13

Identification of internal ribosome entry segment (IRES)-trans-acting factors for the Myc family of IRESs.
Laura C Cobbold, Keith A Spriggs, Stephen J Haines, Helen C Dobbyn, Christopher Hayes, Cornelia H de Moor, Kathryn S Lilley, Martin Bushell, Anne E Willis. Mol Cell Biol 2008
105
13

Translation from unconventional 5' start sites drives tumour initiation.
Ataman Sendoel, Joshua G Dunn, Edwin H Rodriguez, Shruti Naik, Nicholas C Gomez, Brian Hurwitz, John Levorse, Brian D Dill, Daniel Schramek, Henrik Molina,[...]. Nature 2017
177
13

The mechanism of eukaryotic translation initiation and principles of its regulation.
Richard J Jackson, Christopher U T Hellen, Tatyana V Pestova. Nat Rev Mol Cell Biol 2010
13

Translational control of breast cancer plasticity.
Michael Jewer, Laura Lee, Matthew Leibovitch, Guihua Zhang, Jiahui Liu, Scott D Findlay, Krista M Vincent, Kristofferson Tandoc, Dylan Dieters-Castator, Daniela F Quail,[...]. Nat Commun 2020
35
13

Comparative genetics. Systematic discovery of cap-independent translation sequences in human and viral genomes.
Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Alexey A Gritsenko, Noam Stern-Ginossar, Zohar Yakhini, Adina Weinberger, Eran Segal. Science 2016
182
13

Development of a stress response therapy targeting aggressive prostate cancer.
Hao G Nguyen, Crystal S Conn, Yae Kye, Lingru Xue, Craig M Forester, Janet E Cowan, Andrew C Hsieh, John T Cunningham, Charles Truillet, Feven Tameire,[...]. Sci Transl Med 2018
74
13


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.